8TH7: G3BP1 NTF2-like domain

Crystal Structure of the G3BP1 NTF2-like domain bound to the Caprin1 peptide. Determined by X-ray diffraction at 2.88 Å resolution. Released 20 Mar 2024.

Method: X-ray diffraction
Resolution: 2.88 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,417
Mol. weight: 37.22 kDa
Released: 20 Mar 2024

Explore 8TH7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TH7 contains 11 α-helices and 20 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	8-25	18
α-helix	27-33	7
β-strand	34-42	9	1
β-strand	45	1	2
β-strand	51	1	2
α-helix	52-54	3
β-strand	55-56	2	1
α-helix	57-67	11
β-strand	74-85	12	1
β-strand	89-99	11	1
β-strand	105-116	12	1
β-strand	123	1	3
β-strand	124-133	10	1
α-helix	134-136	3

Chain B: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	1-5	5
α-helix	8-25	18
α-helix	30-32	3
β-strand	39-42	4	4
β-strand	45	1	5
β-strand	51	1	5
α-helix	52	1
β-strand	55-56	2	4
α-helix	57-67	11
β-strand	74-85	12	4
β-strand	89-99	11	4
β-strand	106-116	11	4
β-strand	123	1	6
β-strand	124-133	10	4

Chains C and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	12	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras GTPase-activating protein-binding protein 1	A, B	protein	140	Homo sapiens	Q13283 (AlphaFold model)
Caprin-1	C, D	protein	22	Homo sapiens	Q14444 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8TH7_1 Ras GTPase-activating protein-binding protein 1 (chains A, B)
SMVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQK
EIHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGS
VANKFYVHNDIFRYQDEVFG

Sequence of entity 2 (C, D), FASTA

>8TH7_2 Caprin-1 (chains C, D)
QDLMAQMQGPYNFIQDSMLDFE

Primary citation

Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication and pathogenicity. Yang, Z., Johnson, B.A., Meliopoulos, V.A. et al. Cell Rep (2024) 43:113965-113965. DOI 10.1016/j.celrep.2024.113965 · PubMed

Other PDB entries of the same protein (UniProt Q13283 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4FCJ 1.62 Å, Crystal structure of the NTF2-like domain of human G3BP1
3Q90 1.7 Å, Crystal structure of the NTF2 domain of Ras GTPase-activating protein-binding protein 1
8TH1 1.8 Å, Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2…
5FW5 1.92 Å, Crystal structure of human G3BP1 in complex with Semliki Forest Virus nsP3-25 comprising…
6TA7 1.93 Å, Crystal structure of human G3BP1-NTF2 in complex with human CAPRIN1-derived solomon motif
8TH6 2.34 Å, Crystal Structure of the G3BP1 NTF2-like domain bound to USP10 peptide
7SUO 2.35 Å, Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2…
7S17 2.36 Å, Crystal structure of human G3BP1-NTF2 with three mutations- F15W, F33W, and F124W
9CC6 2.4 Å, De novo design of high-affinity protein binders to RNA binding domain of G3bp1
7XHG 2.46 Å, Crystal structure of the NTF2L domain of human G3BP1 in complex with the Caprin-1…
8TH5 2.62 Å, Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2…
9IVQ 2.66 Å, Cryo-EM structure of the CHIKV nsP3 peptide in complex with the NTF2L domain of G3BP1…

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